Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 97 of 318
Found at i:29448453 original size:27 final size:26
Alignment explanation
Indices: 29448418--29448529 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
29448408 AGCATGGCTG
* *
29448418 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
29448444 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
29448472 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
29448499 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
29448526 CCAG
1 CCAG
29448530 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:29448482 original size:54 final size:54
Alignment explanation
Indices: 29448418--29448529 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
29448408 AGCATGGCTG
*
29448418 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
* * * *
29448472 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
29448526 CCAG
1 CCAG
29448530 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:29451154 original size:42 final size:43
Alignment explanation
Indices: 29451105--29451185 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
29451095 TGAGATTACA
* *
29451105 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTTG
1 TGTAAGACCATAGCTAGGATATTGGCATCGATATGAGATTTTG
*
29451147 TGTAAGACCATAGCTAGGCTATTGGCATCGATATGAGAT
1 TGTAAGACCATAGCTAGGATATTGGCATCGATATGAGAT
29451186 CCTATGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 18 0.51
43 17 0.49
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATAGCTAGGATATTGGCATCGATATGAGATTTTG
Found at i:29451197 original size:43 final size:42
Alignment explanation
Indices: 29451108--29451211 Score: 118
Period size: 43 Copynumber: 2.5 Consensus size: 42
29451098 GATTACATGT
* * ** * *
29451108 AAGACCATATCTGGGATATGGCATCGATATGAGATTTTGTGT
1 AAGACCATAGCTAGGATATGGCATCGATATGAGATCCTATGA
*
29451150 AAGACCATAGCTAGGCTATTGGCATCGATATGAGATCCTATGA
1 AAGACCATAGCTAGGATA-TGGCATCGATATGAGATCCTATGA
**
29451193 AAGACCATATTTAGGATAT
1 AAGACCATAGCTAGGATAT
29451212 AGAATTGGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 16 0.31
43 35 0.69
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (42 bp):
AAGACCATAGCTAGGATATGGCATCGATATGAGATCCTATGA
Found at i:29451345 original size:20 final size:20
Alignment explanation
Indices: 29451299--29451349 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
29451289 CGGCAAAGTT
* *
29451299 TAAGTTGTAAAAGACTATGG
1 TAAGTTGTGAAAGACTATAG
* *
29451319 TATGTTGTGAAAGATTATAG
1 TAAGTTGTGAAAGACTATAG
29451339 TAAGTTG-GAAA
1 TAAGTTGTGAAA
29451350 TTTGGTATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.33
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATAG
Found at i:29454595 original size:21 final size:20
Alignment explanation
Indices: 29454571--29454610 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29454561 GTCAAATTGG
29454571 CCACACAGGCGTGTTGCCCTT
1 CCACACAGGCGTG-TGCCCTT
**
29454592 CCACATGGGCGTGTGCCCT
1 CCACACAGGCGTGTGCCCT
29454611 ATTTCTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (20 bp):
CCACACAGGCGTGTGCCCTT
Found at i:29456744 original size:21 final size:21
Alignment explanation
Indices: 29456714--29456756 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29456704 ACAACACAAC
* *
29456714 ATAGCTCCAATTCAAGCATTT
1 ATAGCACCAATTAAAGCATTT
29456735 ATAGCACCAATTAAAGCATTT
1 ATAGCACCAATTAAAGCATTT
29456756 A
1 A
29456757 CATGCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (21 bp):
ATAGCACCAATTAAAGCATTT
Found at i:29461424 original size:40 final size:40
Alignment explanation
Indices: 29461316--29461565 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
29461306 CGGGATTTAA
* * * * *
29461316 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
29461356 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29461396 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29461436 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29461476 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29461516 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29461556 CCGGATATAT
1 CCGGATATAT
29461566 TTCCAATGTT
Statistics
Matches: 193, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 192 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:29469601 original size:40 final size:40
Alignment explanation
Indices: 29469493--29469702 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
29469483 CGGGATTTAA
* * * * *
29469493 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
29469533 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29469573 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29469613 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29469653 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
29469693 CCGGATATAT
1 CCGGATATAT
29469703 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:29482807 original size:28 final size:28
Alignment explanation
Indices: 29482761--29482816 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
29482751 CATTAACAAT
* *
29482761 ACAGTCTGGGCCTAAGCCCTATACAGTA
1 ACAGTCTGGGCCTAAGCCCAAAACAGTA
* **
29482789 ACAGTGTGGGCCTTTGCCCAAAACAGTA
1 ACAGTCTGGGCCTAAGCCCAAAACAGTA
29482817 TAATCACAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTCTGGGCCTAAGCCCAAAACAGTA
Found at i:29489558 original size:49 final size:49
Alignment explanation
Indices: 29489494--29489676 Score: 219
Period size: 49 Copynumber: 3.7 Consensus size: 49
29489484 CAAAGCAATT
* *
29489494 TGGTACACATAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATC
* * *
29489543 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATC
* * * *
29489594 AGGTAGTA--TAGTAGCCTGCACTTAGTACTACACATGCGGCCAATAAT-
1 TGGTA-CACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATC
*
29489641 TCGGTACACGTAGTAGCCTACACTTAGTACTACACA
1 T-GGTACACGTAGTAGCCTGCACTTAGTACTACACA
29489677 CGTGACCTCA
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
47 1 0.01
48 7 0.06
49 64 0.57
50 31 0.27
51 9 0.08
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (49 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATC
Found at i:29489673 original size:99 final size:99
Alignment explanation
Indices: 29489502--29489681 Score: 308
Period size: 99 Copynumber: 1.8 Consensus size: 99
29489492 TTTGGTACAC
* * *
29489502 ATAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCTACACTT
29489567 AGTACTACACACGTGATCGAAGTTATCAGGTAGT
66 AGTACTACACACGTGATCGAAGTTATCAGGTAGT
*
29489601 ATAGTAGCCTGCACTTAGTACTACACATGCGGCCAATAAT-TCGGTACACGTAGTAGCCTACACT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCT-GGTACACGTAGTAGCCTACACT
29489665 TAGTACTACACACGTGA
65 TAGTACTACACACGTGA
29489682 CCTCACAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 1 0.01
99 75 0.99
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (99 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCTACACTT
AGTACTACACACGTGATCGAAGTTATCAGGTAGT
Found at i:29495020 original size:50 final size:50
Alignment explanation
Indices: 29494956--29495151 Score: 241
Period size: 50 Copynumber: 3.9 Consensus size: 50
29494946 AGCCAAGGCT
* **
29494956 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATA
* * * * *
29495006 ATCTGATACACATAGTAGCCTGCACTTAGTACGACACACGTGATCGAAGTT
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-TA
* * * *
29495057 ATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATA
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATA
* * *
29495106 ATCTGGTACACGTAGCAGCCTGCACTTAGTACTACACACATGACCT
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT
29495152 CACTATAGAT
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 39 0.32
50 45 0.37
51 38 0.31
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (50 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATA
Found at i:29496267 original size:13 final size:13
Alignment explanation
Indices: 29496251--29496275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29496241 CGAACGAAAT
29496251 TTTCATGAAATCA
1 TTTCATGAAATCA
29496264 TTTCATGAAATC
1 TTTCATGAAATC
29496276 GTAGACCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTCATGAAATCA
Found at i:29498633 original size:42 final size:42
Alignment explanation
Indices: 29498574--29498659 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 42
29498564 CAAGAAAATG
*
29498574 GTTTTTCTAACCCAACACTATCAATAATAAATTGAATCCTAA
1 GTTTTTCTAACCCAACACTATCAATAATAAAATGAATCCTAA
29498616 GTTTTTCTTAA-CCAACACTATCAATAATAAAATGAATCCTAA
1 GTTTTTC-TAACCCAACACTATCAATAATAAAATGAATCCTAA
29498658 GT
1 GT
29498660 ATACCCGATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (42 bp):
GTTTTTCTAACCCAACACTATCAATAATAAAATGAATCCTAA
Found at i:29503944 original size:40 final size:40
Alignment explanation
Indices: 29503844--29504014 Score: 218
Period size: 40 Copynumber: 4.2 Consensus size: 40
29503834 AACATTGGAA
29503844 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29503884 ATATAATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATAT-ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29503925 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29503964 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29504005 CTATATCCGG
1 ATATATCCGG
29504015 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.02
40 69 0.62
41 40 0.36
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29511997 original size:40 final size:40
Alignment explanation
Indices: 29511942--29512111 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
29511932 AACATTGGAA
29511942 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29511982 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29512022 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29512061 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29512102 CTATATCCGG
1 ATATATCCGG
29512112 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29520435 original size:27 final size:27
Alignment explanation
Indices: 29520404--29520457 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29520394 ACTAAACCCC
29520404 TTAAATACCTAAGGGGAATGAAACCTA
1 TTAAATACCTAAGGGGAATGAAACCTA
29520431 TTAAATACCTAAGGGGAATGAAACCTA
1 TTAAATACCTAAGGGGAATGAAACCTA
29520458 AGACGGATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (27 bp):
TTAAATACCTAAGGGGAATGAAACCTA
Found at i:29528848 original size:12 final size:13
Alignment explanation
Indices: 29528812--29528849 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29528802 AAATATTTTA
29528812 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
29528825 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
29528839 CTTG-TCTTAAT
1 CTTGTTCTTAAT
29528850 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:29534431 original size:27 final size:26
Alignment explanation
Indices: 29534401--29534451 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
29534391 CCCAAATTGT
*
29534401 TAAAATGACTGTTATACCCCTATGAGG
1 TAAAATGACTGATAT-CCCCTATGAGG
*
29534428 TAAAATGACTGATATGCCCTATGA
1 TAAAATGACTGATATCCCCTATGA
29534452 TATGTATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (26 bp):
TAAAATGACTGATATCCCCTATGAGG
Found at i:29542482 original size:45 final size:45
Alignment explanation
Indices: 29542431--29542517 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
29542421 AGGATTTTTG
* * * *
29542431 GTATGTGTTTTCGGGTAAAACCATGTCTGGGACGTCGGCATCAAT
1 GTATGTGGTTACGGGTAAAACCATGTCTGGGACATCGACATCAAT
*
29542476 GTATGTGGTTACGTGTAAAACCATGTCTGGGACATCGACATC
1 GTATGTGGTTACGGGTAAAACCATGTCTGGGACATCGACATC
29542518 GTATTTGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (45 bp):
GTATGTGGTTACGGGTAAAACCATGTCTGGGACATCGACATCAAT
Found at i:29544348 original size:41 final size:41
Alignment explanation
Indices: 29544291--29544369 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
29544281 AAAGCCACCA
*
29544291 GTGGATCCACAGTCGTCAAGCAACCATGCGATCCTCAACCG
1 GTGGATCCACAGTCGTCAAGCAACCATACGATCCTCAACCG
* *
29544332 GTGGATCGACGGTCGTCAAGCAACCATACGATCCTCAA
1 GTGGATCCACAGTCGTCAAGCAACCATACGATCCTCAA
29544370 TTTCTTCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.18
Consensus pattern (41 bp):
GTGGATCCACAGTCGTCAAGCAACCATACGATCCTCAACCG
Found at i:29544611 original size:29 final size:29
Alignment explanation
Indices: 29544578--29544633 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
29544568 TCTTTTTACC
*
29544578 TATTAAGGGTATTTTAGTCATTTCACCCT
1 TATTAAGGGTATTTCAGTCATTTCACCCT
29544607 TATTAAGGGTATTTCAGTCATTTCACC
1 TATTAAGGGTATTTCAGTCATTTCACC
29544634 TTACAAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (29 bp):
TATTAAGGGTATTTCAGTCATTTCACCCT
Found at i:29544648 original size:29 final size:29
Alignment explanation
Indices: 29544582--29544643 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
29544572 TTTACCTATT
* *
29544582 AAGGGTATTTTAGTCATTTCACCCTTATT
1 AAGGGTATTTCAGTCATTTCACCCTTATC
29544611 AAGGGTATTTCAGTCATTTCA-CCTTA-C
1 AAGGGTATTTCAGTCATTTCACCCTTATC
29544638 AAGGGT
1 AAGGGT
29544644 GTATTGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 20 0.65
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (29 bp):
AAGGGTATTTCAGTCATTTCACCCTTATC
Found at i:29544739 original size:27 final size:26
Alignment explanation
Indices: 29544695--29544902 Score: 150
Period size: 27 Copynumber: 7.7 Consensus size: 26
29544685 GCAAACTAAT
* *
29544695 GGTATTTTTGTAATTTTTAAAAGTCAAC
1 GGTATTTCTGTAA-TTTTAAAA-TCAAG
* * *
29544723 GGTATTTTTGTAATTTTGTAAATCAGG
1 GGTATTTCTGTAATTTT-AAAATCAAG
* *
29544750 GGTATTTCTGTAATTTTCCAAATTAAG
1 GGTATTTCTGTAATTTT-AAAATCAAG
* * *
29544777 GGTATTTCGGTAATTTTTCAAATCAGG
1 GGTATTTCTGTAA-TTTTAAAATCAAG
* *
29544804 GGTATTT-TGGTAATTTTACAATTCGAG
1 GGTATTTCT-GTAATTTTA-AAATCAAG
**
29544831 GGTATTTC-GTTAATTTTACAGGTCAAG
1 GGTATTTCTG-TAATTTTA-AAATCAAG
* * * *
29544858 GGTATTTCGGTAATTTTTCAAGTCAAT
1 GGTATTTCTGTAA-TTTTAAAATCAAG
29544885 GGTATTTCTGTAATTTTA
1 GGTATTTCTGTAATTTTA
29544903 CAAACCAGGA
Statistics
Matches: 148, Mismatches: 24, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
26 9 0.06
27 114 0.77
28 25 0.17
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (26 bp):
GGTATTTCTGTAATTTTAAAATCAAG
Found at i:29544834 original size:81 final size:79
Alignment explanation
Indices: 29544657--29544911 Score: 242
Period size: 81 Copynumber: 3.1 Consensus size: 79
29544647 TTGGTAAATC
* * * * * ** *
29544657 TACAAACCAAGGGTATTTCGATAAATTTGCAAACTAATGGTATTTTTGTAATTTTTAAAAGTCAA
1 TACAAATC-AGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCGGTAATTTTTCAAA-TCAA
29544722 CGGTATTTTTGTAATTT
64 CGGTA-TTTTGTAATTT
** * *
29544739 TGTAAATCAGGGGTATTTCTG-TAATTTTCCAAATTAAGGGTATTTCGGTAATTTTTCAAATCAG
1 TACAAATCA-GGGTATTTC-GATAATTTTACAAATTAAGGGTATTTCGGTAATTTTTCAAATCAA
*
29544803 GGGTATTTTGGTAATTT
64 CGGTATTTT-GTAATTT
* * ** * * *
29544820 TACAATTCGAGGGTATTTCGTTAATTTTACAGGTCAAGGGTATTTCGGTAATTTTTCAAGTCAAT
1 TACAAATC-AGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCGGTAATTTTTCAAATCAAC
29544885 GGTATTTCTGTAATTT
65 GGTATTT-TGTAATTT
*
29544901 TACAAACCAGG
1 TACAAATCAGG
29544912 AGCATTTTAG
Statistics
Matches: 143, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
80 8 0.06
81 86 0.60
82 48 0.34
83 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (79 bp):
TACAAATCAGGGTATTTCGATAATTTTACAAATTAAGGGTATTTCGGTAATTTTTCAAATCAACG
GTATTTTGTAATTT
Found at i:29544902 original size:54 final size:54
Alignment explanation
Indices: 29544695--29544911 Score: 211
Period size: 54 Copynumber: 4.0 Consensus size: 54
29544685 GCAAACTAAT
** * * * **
29544695 GGTATTTTTGTAATTTTTAAAAGTCAACGGTATTTTTGTAATTTTGTAAATCAGG
1 GGTATTTCGGTAATTTTT-CAAGTCAAGGGTATTTCTGTAATTTTACAAATCAGG
* * * * * *
29544750 GGTATTTCTGTAATTTTCCAAATTAAGGGTATTTCGGTAATTTTTCAAATCAGG
1 GGTATTTCGGTAATTTTTCAAGTCAAGGGTATTTCTGTAATTTTACAAATCAGG
* * * * ** *
29544804 GGTATTTTGGTAATTTTACAATTCGAGGGTATTTC-GTTAATTTTACAGGTCAAG
1 GGTATTTCGGTAATTTTTCAAGTCAAGGGTATTTCTG-TAATTTTACAAATCAGG
* *
29544858 GGTATTTCGGTAATTTTTCAAGTCAATGGTATTTCTGTAATTTTACAAACCAGG
1 GGTATTTCGGTAATTTTTCAAGTCAAGGGTATTTCTGTAATTTTACAAATCAGG
29544912 AGCATTTTAG
Statistics
Matches: 131, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 1 0.01
54 113 0.86
55 17 0.13
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (54 bp):
GGTATTTCGGTAATTTTTCAAGTCAAGGGTATTTCTGTAATTTTACAAATCAGG
Found at i:29544925 original size:54 final size:54
Alignment explanation
Indices: 29544664--29544926 Score: 199
Period size: 54 Copynumber: 4.9 Consensus size: 54
29544654 ATCTACAAAC
* * * ** * *
29544664 CAAGGGTATTTC-GATAAATTTGCAAACTAATGGTATTTTTGTAATTTTTAAAAGT
1 CAAGGGTATTTCTG-TAATTTTACAAACCAGGGGTATTTTGGTAATTTTT-CAAGT
* * ** * * *
29544719 CAACGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTCT-GTAATTTTCCAAAT
1 CAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTT-TGGTAATTTTTCAAGT
* * * * * *
29544773 TAAGGGTATTTCGGTAATTTTTCAAATCAGGGGTATTTTGGTAATTTTACAATT
1 CAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTTCAAGT
* *** * *
29544827 CGAGGGTATTTC-GTTAATTTTACAGGTCAAGGGTATTTCGGTAATTTTTCAAGT
1 CAAGGGTATTTCTG-TAATTTTACAAACCAGGGGTATTTTGGTAATTTTTCAAGT
* * * *
29544881 CAATGGTATTTCTGTAATTTTACAAACCAGGAGCATTTTAGTAATT
1 CAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTTGGTAATT
29544927 CTATCCTACC
Statistics
Matches: 165, Mismatches: 38, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
53 2 0.01
54 124 0.75
55 37 0.22
56 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (54 bp):
CAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTTCAAGT
Found at i:29544961 original size:27 final size:28
Alignment explanation
Indices: 29544906--29544962 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
29544896 AATTTTACAA
*
29544906 ACCAGGAGCATTTTAGTAATTCTATCCT
1 ACCAGGAGCATTTTAGTAATTCTAGCCT
29544934 ACCAGG-GCATTTTAGTAATAT-TAGCCT
1 ACCAGGAGCATTTTAGTAAT-TCTAGCCT
29544961 AC
1 AC
29544963 AGATATGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (28 bp):
ACCAGGAGCATTTTAGTAATTCTAGCCT
Found at i:29551220 original size:32 final size:32
Alignment explanation
Indices: 29551174--29551249 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 32
29551164 AAAATGCATA
*
29551174 AAACCATATGTTAGATGGGCATTTAAACCAATCT
1 AAACCA-A-GTTAGATAGGCATTTAAACCAATCT
29551208 AAACCAAGTTAGATAGGCATTTAAACCAATCT
1 AAACCAAGTTAGATAGGCATTTAAACCAATCT
29551240 AAACCAAGTT
1 AAACCAAGTT
29551250 CAATTCATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 34 0.83
33 1 0.02
34 6 0.15
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (32 bp):
AAACCAAGTTAGATAGGCATTTAAACCAATCT
Found at i:29552937 original size:16 final size:16
Alignment explanation
Indices: 29552916--29552947 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29552906 AGTGTAACGC
*
29552916 CCCAAAAATCCTGAAA
1 CCCAAAAATCCCGAAA
29552932 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
29552948 TCTTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:29554536 original size:28 final size:29
Alignment explanation
Indices: 29554425--29554542 Score: 143
Period size: 29 Copynumber: 4.1 Consensus size: 29
29554415 GTGAGCATGA
*
29554425 ATATGAATGTGA-TTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
29554453 ATATAAATGTTATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
29554482 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* * *
29554511 ATATGAATATGA-ATGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
29554539 ATAT
1 ATAT
29554543 ACAGGTATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 29 0.37
29 48 0.62
30 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:29554536 original size:57 final size:57
Alignment explanation
Indices: 29554433--29554548 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
29554423 GAATATGAAT
* * *
29554433 GTGATTGGGCCTAACGGGCCATATAAATGTTATTTGGGCCTAATGGGCCATATACAG
1 GTGATTGGGCCTAACGGGCCATATAAATATGATATGGGCCTAATGGGCCATATACAG
* * *
29554490 GTGATTTGGGCCTAATGGGCCATATGAATATGA-ATGGGCTTAATGGGCCATATACAG
1 GTGA-TTGGGCCTAACGGGCCATATAAATATGATATGGGCCTAATGGGCCATATACAG
29554547 GT
1 GT
29554549 ATGTGAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 28 0.54
58 24 0.46
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (57 bp):
GTGATTGGGCCTAACGGGCCATATAAATATGATATGGGCCTAATGGGCCATATACAG
Found at i:29570738 original size:43 final size:42
Alignment explanation
Indices: 29570677--29570792 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 42
29570667 ATAAGCTCGT
* **
29570677 ACAATGCCATATCCCAGATATGGTCTTAC-CTGTTA-TCACATA
1 ACAATGCCATGTCCCAGATATGGTCTTACAC-GAAATTCA-ATA
* * *
29570719 TCAATGCCACTGTCCCAGATAGGGTCTTACACGAAATTGAATA
1 ACAATGCCA-TGTCCCAGATATGGTCTTACACGAAATTCAATA
*
29570762 ACAATGCCAATGTCCCAGACATGGTCTTACA
1 ACAATGCC-ATGTCCCAGATATGGTCTTACA
29570793 AGTAATCACA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 8 0.13
43 49 0.80
44 4 0.07
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
ACAATGCCATGTCCCAGATATGGTCTTACACGAAATTCAATA
Found at i:29582471 original size:49 final size:49
Alignment explanation
Indices: 29582382--29582527 Score: 206
Period size: 49 Copynumber: 3.0 Consensus size: 49
29582372 CCCTTCGGGA
* * * ** * *
29582382 CTTATCACAT-T-TATACACTTCCACATCCATCAGGTTGGCCACTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
29582429 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
29582478 CTTATCACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
29582527 C
1 C
29582528 ACTTTCTCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 10 0.11
48 1 0.01
49 78 0.88
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29582536 original size:32 final size:32
Alignment explanation
Indices: 29582495--29582559 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29582485 CATATATACA
29582495 CACTTTCTCATTCATCACATCGGCCATTAGGC
1 CACTTTCTCATTCATCACATCGGCCATTAGGC
29582527 CACTTTCTCATTCATCACATCGGCCATTAGGC
1 CACTTTCTCATTCATCACATCGGCCATTAGGC
29582559 C
1 C
29582560 TTATCACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (32 bp):
CACTTTCTCATTCATCACATCGGCCATTAGGC
Found at i:29582544 original size:81 final size:81
Alignment explanation
Indices: 29582446--29582608 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
29582436 CATATATACA
*
29582446 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCTCATTCATC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATC
29582511 ACATCGGCCATTAGGC
66 ACATCGGCCATTAGGC
*
29582527 CACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATC
29582592 ACATCGGCCATTAGGC
66 ACATCGGCCATTAGGC
29582608 C
1 C
29582609 TTATCACATA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.31
Consensus pattern (81 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATC
ACATCGGCCATTAGGC
Found at i:29582588 original size:49 final size:49
Alignment explanation
Indices: 29582527--29582818 Score: 548
Period size: 49 Copynumber: 6.0 Consensus size: 49
29582517 GCCATTAGGC
*
29582527 CACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
29582576 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
29582625 CACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
29582674 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
29582723 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
* *
29582772 CACTTTCACATTCATCTCATCGGCCATTAGGCCTTACCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
29582819 TATCTCATAC
Statistics
Matches: 238, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 238 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (49 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
Found at i:29582630 original size:130 final size:130
Alignment explanation
Indices: 29582418--29582657 Score: 471
Period size: 130 Copynumber: 1.8 Consensus size: 130
29582408 CCATCAGGTT
29582418 GGCCACTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 GGCCACTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
29582483 CACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGCCACTTTCTCATTCATCACATC
66 CACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGCCACTTTCTCATTCATCACATC
*
29582548 GGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 GGCCACTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
29582613 CACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGCC
66 CACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGCC
29582658 TTATCACATA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (130 bp):
GGCCACTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
CACATATATACACACTTTCTCATTCATCACATCGGCCATTAGGCCACTTTCTCATTCATCACATC
Found at i:29585979 original size:21 final size:22
Alignment explanation
Indices: 29585946--29585988 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29585936 CAAGTCATAA
29585946 ATTTCCATCCAAAT-TAAAGTC
1 ATTTCCATCCAAATATAAAGTC
* *
29585967 ATTTGCATTCAAATATAAAGTC
1 ATTTCCATCCAAATATAAAGTC
29585989 CCTAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (22 bp):
ATTTCCATCCAAATATAAAGTC
Found at i:29590696 original size:19 final size:19
Alignment explanation
Indices: 29590658--29590697 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29590648 CATCCGTTTA
* *
29590658 AATAGTACTTCATCCATAT
1 AATAGTAATTCAACCATAT
*
29590677 AATAGTAATTCAACCGTAT
1 AATAGTAATTCAACCATAT
29590696 AA
1 AA
29590698 CACATAGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (19 bp):
AATAGTAATTCAACCATAT
Found at i:29590883 original size:25 final size:25
Alignment explanation
Indices: 29590829--29590886 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
29590819 TTCTACTCGT
*
29590829 TTGAGCTATGATCAGTAAGCTCCTC
1 TTGAGCTATGATCAGTAAGCTCCTA
*
29590854 CTGAGCTGATGGAT-AGTAAGCT-CTA
1 TTGAGCT-AT-GATCAGTAAGCTCCTA
29590879 TTGAGCTA
1 TTGAGCTA
29590887 AAACGGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 1 0.04
25 14 0.50
26 10 0.36
27 3 0.11
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
TTGAGCTATGATCAGTAAGCTCCTA
Found at i:29592174 original size:38 final size:38
Alignment explanation
Indices: 29592123--29592198 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
29592113 ACGTGTAAGA
29592123 CCATATCTTGGATATGGCATCAATATGAGATTTTGTGT
1 CCATATCTTGGATATGGCATCAATATGAGATTTTGTGT
*
29592161 CCATATCTTGGATATGGCATCGATATGAGATTTTGTGT
1 CCATATCTTGGATATGGCATCAATATGAGATTTTGTGT
29592199 AAGACTATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (38 bp):
CCATATCTTGGATATGGCATCAATATGAGATTTTGTGT
Found at i:29594900 original size:48 final size:49
Alignment explanation
Indices: 29594833--29594932 Score: 130
Period size: 48 Copynumber: 2.0 Consensus size: 49
29594823 GCTATCGGCT
* * * *
29594833 TCGATATGCATGATCCCATGTAAGACCATGTTTGGGACATAGCATTGGCA
1 TCGATATG-ATGATCCCATGTAAAACCATATCTAGGACATAGCATTGGCA
* *
29594883 TCGATATG-TGATCCCATGTAAAACCATATCTAGGATATGGCATTGGCA
1 TCGATATGATGATCCCATGTAAAACCATATCTAGGACATAGCATTGGCA
29594931 TC
1 TC
29594933 CTACTATGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
48 36 0.82
50 8 0.18
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (49 bp):
TCGATATGATGATCCCATGTAAAACCATATCTAGGACATAGCATTGGCA
Found at i:29596348 original size:24 final size:25
Alignment explanation
Indices: 29596293--29596359 Score: 100
Period size: 24 Copynumber: 2.7 Consensus size: 25
29596283 TTTTAATAAG
*
29596293 TGGGGCAAAAGCCCTTTTCGGTAAAC
1 TGGGGC-AAAGCCCTTTTCAGTAAAC
29596319 TGGGGCAAAGCCCTTTTCAGT-AAC
1 TGGGGCAAAGCCCTTTTCAGTAAAC
*
29596343 TGGGGCATAGCCCTTTT
1 TGGGGCAAAGCCCTTTT
29596360 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 19 0.49
25 14 0.36
26 6 0.15
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTCAGTAAAC
Found at i:29596420 original size:11 final size:11
Alignment explanation
Indices: 29596404--29596453 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 11
29596394 CATTATGAAT
29596404 ATATCATGTAC
1 ATATCATGTAC
29596415 ATATCA--TAC
1 ATATCATGTAC
*
29596424 ATATCATGTGC
1 ATATCATGTAC
29596435 ATATCA--TAC
1 ATATCATGTAC
29596444 ATATCATGTA
1 ATATCATGTA
29596454 TATCAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 17 0.52
11 16 0.48
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (11 bp):
ATATCATGTAC
Found at i:29596429 original size:20 final size:20
Alignment explanation
Indices: 29596404--29596453 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
29596394 CATTATGAAT
29596404 ATATCATGTACATATCATAC
1 ATATCATGTACATATCATAC
*
29596424 ATATCATGTGCATATCATAC
1 ATATCATGTACATATCATAC
29596444 ATATCATGTA
1 ATATCATGTA
29596454 TATCAGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (20 bp):
ATATCATGTACATATCATAC
Found at i:29605395 original size:48 final size:48
Alignment explanation
Indices: 29605324--29605547 Score: 221
Period size: 48 Copynumber: 4.7 Consensus size: 48
29605314 GCATGAACCC
*
29605324 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAAATGTGATCCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCA
* *
29605372 ATGTAAGACCATGTCTGGGACATGACATTGGCATCAATATGAGA--CA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCA
* * * * *
29605418 TCGTGTAAGACCATAG-CTGGG-C-T---ATCGGCTTCGATATGCATGATCCC
1 --ATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCAATATG--TGATCCA
* *
29605465 ATGTAAGACCATGTTTGGGACATGGCATTGGCATCAATATGTGATCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCA
** * *
29605513 ATGTAAGACCACATCTGGGATATGGAATTGGCATC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCATC
29605548 CTACTATGTG
Statistics
Matches: 144, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
43 12 0.08
44 1 0.01
45 17 0.12
46 4 0.03
47 3 0.02
48 94 0.65
49 1 0.01
50 12 0.08
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (48 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTGATCCA
Found at i:29613221 original size:42 final size:42
Alignment explanation
Indices: 29613162--29613283 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
29613152 TTAGGGTTGT
* *
29613162 TGAGATTATGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGATTCTGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
29613204 TGAGATTCTGTGTAAGACCATAGCTGGGCTATTGGCACCGATA
1 TGAGATTCTGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* * **
29613247 TGAAATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTCTGTGTAAGACCATATCTGGGATATGGCAT
29613284 TGGTATGATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 32 0.48
43 35 0.52
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCTGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:29613394 original size:20 final size:20
Alignment explanation
Indices: 29613366--29613412 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29613356 GGGCAAAGTT
*
29613366 TAAGTTGTGAAAGCCTATGG
1 TAAGTTGTGAAAGACTATGG
* *
29613386 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
29613406 TAAGTTG
1 TAAGTTG
29613413 CAAGTTTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:29616875 original size:38 final size:38
Alignment explanation
Indices: 29616819--29616892 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
29616809 ATTAAGCAGC
29616819 CAATCCACAACATCTCATACACATTTTATACCAATTTT
1 CAATCCACAACATCTCATACACATTTTATACCAATTTT
* *
29616857 CAATCCACAACATTTCATACACATTTTATATCAATT
1 CAATCCACAACATCTCATACACATTTTATACCAATT
29616893 CAACATAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (38 bp):
CAATCCACAACATCTCATACACATTTTATACCAATTTT
Found at i:29617587 original size:19 final size:19
Alignment explanation
Indices: 29617513--29617598 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 19
29617503 CACTCTCAAT
*
29617513 CATATAAACAGTAATTCATT
1 CATAT-AACAGTAATTCATC
* *
29617533 C-GATAACAGTAACTCATC
1 CATATAACAGTAATTCATC
* * * *
29617551 CGTTTAAATAGTACTTCATC
1 CATAT-AACAGTAATTCATC
*
29617571 CATATAACAGTAATTCATT
1 CATATAACAGTAATTCATC
29617590 CATATAACA
1 CATATAACA
29617599 CATAGCTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
18 13 0.25
19 23 0.45
20 15 0.29
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (19 bp):
CATATAACAGTAATTCATC
Found at i:29619925 original size:41 final size:42
Alignment explanation
Indices: 29619869--29619971 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
29619859 CAATGCCAAC
* *
29619869 GTCCCAGAC-GTGGTCTTACATGTAGTCAAATATCGATGCC-A-
1 GTCCCAGACAG-GGTCTTACATGAAATCAAATAT-GATGCCGAT
29619910 GTCCCAGACAGGGTCTTACATGAAATCAAATATGATGCCGAT
1 GTCCCAGACAGGGTCTTACATGAAATCAAATATGATGCCGAT
* * *
29619952 GTCTCAAACATGGTCTTACA
1 GTCCCAGACAGGGTCTTACA
29619972 CATAAATCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 6 0.11
41 30 0.56
42 18 0.33
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACATGAAATCAAATATGATGCCGAT
Found at i:29620402 original size:8 final size:8
Alignment explanation
Indices: 29620389--29620413 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29620379 AAATTAGCCC
29620389 TCACATTT
1 TCACATTT
29620397 TCACATTT
1 TCACATTT
29620405 TCACATTT
1 TCACATTT
29620413 T
1 T
29620414 AACACTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:29640625 original size:43 final size:42
Alignment explanation
Indices: 29640568--29640668 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
29640558 CGATTTCATG
* * *
29640568 TAAGACTATGTCTGGGACATGGCTTCGAAAATGAGACTTCGTA
1 TAAGACTATATCTGGGACATGGCATCG-AAATGAGACATCGTA
* * *
29640611 TAAGACTATATCTGGGATATGGCATCGATATGAGACATCGTG
1 TAAGACTATATCTGGGACATGGCATCGAAATGAGACATCGTA
* *
29640653 TAAGACCATAGCTGGG
1 TAAGACTATATCTGGG
29640669 CTATTGGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
42 26 0.52
43 24 0.48
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (42 bp):
TAAGACTATATCTGGGACATGGCATCGAAATGAGACATCGTA
Found at i:29640657 original size:42 final size:42
Alignment explanation
Indices: 29640526--29640714 Score: 139
Period size: 43 Copynumber: 4.5 Consensus size: 42
29640516 AGATTCCGTA
* * ** * ** *
29640526 TAAGACCATATTTGGGATATGGCATTGGCATGCGATTTCATG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGACATCGTG
* * * * * * *
29640568 TAAGACTATGTCTGGGACATGGCTTCGAAAATGAGACTTCGTA
1 TAAGACCATATCTGGGATATGGCATCG-ATATGAGACATCGTG
*
29640611 TAAGACTATATCTGGGATATGGCATCGATATGAGACATCGTG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGACATCGTG
* * * * *
29640653 TAAGACCATAGCTGGGCTATTGGTATCGATAT-ATGATCCT-ATG
1 TAAGACCATATCTGGGATA-TGGCATCGATATGA-GA-CATCGTG
29640696 TAAGACCATATCTGGGATA
1 TAAGACCATATCTGGGATA
29640715 CGGAATTGAC
Statistics
Matches: 117, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
42 50 0.43
43 65 0.56
44 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
TAAGACCATATCTGGGATATGGCATCGATATGAGACATCGTG
Found at i:29643336 original size:40 final size:39
Alignment explanation
Indices: 29643171--29643354 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29643161 AAATTGAATG
* * *
29643171 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29643211 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29643251 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29643291 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29643330 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29643355 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29643379 original size:80 final size:81
Alignment explanation
Indices: 29643211--29643399 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29643201 GCTGGAAATT
* * * *
29643211 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29643276 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29643292 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29643355 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29643371 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29643400 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29649697 original size:40 final size:39
Alignment explanation
Indices: 29649529--29649699 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
29649519 AGAAATTGAA
* *
29649529 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
29649569 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
29649609 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
29649649 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
29649689 TGATATCCGGG
1 TGATATCCGGG
29649700 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:29654749 original size:40 final size:39
Alignment explanation
Indices: 29654584--29654767 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29654574 AAATTGAATG
* * *
29654584 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29654624 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29654664 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29654704 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29654743 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29654768 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29654792 original size:80 final size:81
Alignment explanation
Indices: 29654624--29654812 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29654614 GCTGGAAATT
* * * *
29654624 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29654689 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29654705 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29654768 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29654784 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29654813 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29664315 original size:49 final size:50
Alignment explanation
Indices: 29664236--29664470 Score: 262
Period size: 49 Copynumber: 4.7 Consensus size: 50
29664226 GGTCACGTGC
* * *
29664236 GTAGTACTGAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCATGT
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCGCATGT
* * * * ***
29664285 GTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCATGTGT
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTAGGTCGCATGT
* ** **
29664336 GTAGTACTAAGTGCAGGCTACTACGTGTTTCAGATGGTTAGGT--CATGTTT
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCGCATG--T
*
29664386 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTTGCATGT
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCGCATGT
*
29664435 GTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
29664471 GCCTTGTCTA
Statistics
Matches: 155, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
48 2 0.01
49 72 0.46
50 41 0.26
51 40 0.26
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
GTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCGCATGT
Found at i:29664416 original size:101 final size:97
Alignment explanation
Indices: 29664236--29664470 Score: 285
Period size: 101 Copynumber: 2.4 Consensus size: 97
29664226 GGTCACGTGC
* *
29664236 GTAGTACTGAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGCAG
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTC-CATGTGTAGTACTAAGTGCAG
*
29664301 GCTACTATGCGTACCCGATAACTTCGAT-CATGTGT
65 GCTACTATGCGTACCAGATAA-TTCGATGCA--TGT
** **
29664336 GTAGTACTAAGTGCAGGCTACTACGTGTTTCAGATGGTTAGGT-CATGTTTGTAGTACTAAGTGC
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCCATG--TGTAGTACTAAGTGC
* * *
29664400 AGGCTACTATGTGTACCAGATAATTGGTTGCATGT
63 AGGCTACTATGCGTACCAGATAATTCGATGCATGT
* *
29664435 GTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
29664471 GCCTTGTCTA
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
99 38 0.33
100 37 0.32
101 41 0.35
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (97 bp):
GTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCCATGTGTAGTACTAAGTGCAGG
CTACTATGCGTACCAGATAATTCGATGCATGT
Found at i:29667663 original size:29 final size:29
Alignment explanation
Indices: 29667603--29667677 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
29667593 TCATATTCAC
* * **
29667603 ATGGCCCATTTGGCCCAAATCACCTGTAT
1 ATGGCCCATTAGGCCTAAATCAAATGTAT
* *
29667632 ATGGCCCATTAGGCCTAAATCAAATTTTT
1 ATGGCCCATTAGGCCTAAATCAAATGTAT
**
29667661 ATGGCCCGGTAGGCCTA
1 ATGGCCCATTAGGCCTA
29667678 GTCACATTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (29 bp):
ATGGCCCATTAGGCCTAAATCAAATGTAT
Found at i:29669116 original size:40 final size:39
Alignment explanation
Indices: 29669071--29669278 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
29669061 CGGAATACAA
*
29669071 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
29669111 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
29669151 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
29669191 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
29669231 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
29669271 CCGGATAT
1 CCGGATAT
29669279 CATTTAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:29669218 original size:80 final size:81
Alignment explanation
Indices: 29669071--29669276 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
29669061 CGGAATACAA
* * * *
29669071 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
29669135 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
29669151 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAG-TC-ACTAGCATAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAGAACGACTAGCACAAA
*
29669214 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* * ** * *
29669231 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
29669277 ATCATTTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 104 0.95
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:29673148 original size:28 final size:28
Alignment explanation
Indices: 29673116--29673214 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
29673106 GCAATAAGCC
*
29673116 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
29673144 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
29673172 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
29673201 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29673215 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:29680826 original size:28 final size:28
Alignment explanation
Indices: 29680794--29680892 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
29680784 GCAATAAGCC
*
29680794 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
29680822 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
29680850 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
29680879 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29680893 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:29687714 original size:40 final size:39
Alignment explanation
Indices: 29687669--29687876 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
29687659 CGGAATACAA
*
29687669 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
29687709 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
29687749 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
29687789 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
29687829 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
29687869 CCGGATAT
1 CCGGATAT
29687877 CATTTAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:29687816 original size:80 final size:81
Alignment explanation
Indices: 29687669--29687874 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
29687659 CGGAATACAA
* * * *
29687669 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
29687733 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
29687749 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAG-TC-ACTAGCATAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAGAACGACTAGCACAAA
*
29687812 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* * ** * *
29687829 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
29687875 ATCATTTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 104 0.95
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:29691029 original size:16 final size:16
Alignment explanation
Indices: 29691004--29691037 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29690994 AAGTTCGGGA
*
29691004 TTTTGGGATTTTTAGG
1 TTTTGAGATTTTTAGG
*
29691020 TTTTGAGATTTTTGGG
1 TTTTGAGATTTTTAGG
29691036 TT
1 TT
29691038 GTTACAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.29, T:0.59
Consensus pattern (16 bp):
TTTTGAGATTTTTAGG
Found at i:29693992 original size:29 final size:29
Alignment explanation
Indices: 29693926--29694023 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 29
29693916 TTCACATACC
* * *
29693926 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCAAA
** * **
29693954 T-TCACGTGGCCCATTTGGCCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCAAA
*
29693983 TGTATATGGCCCATTAGGCCTAAATCAAA
1 TGTATATGGCCCATTAGGCCCAAATCAAA
*
29694012 TTTATATGGCCC
1 TGTATATGGCCC
29694024 GGTAGGCCTA
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.02
28 15 0.28
29 37 0.69
30 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCAAA
Found at i:29694126 original size:17 final size:18
Alignment explanation
Indices: 29694104--29694150 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
29694094 TTGCCTATTA
29694104 TGGGCCCA-ATAGCCCAT
1 TGGGCCCATATAGCCCAT
*
29694121 TGGGCCCATTTAGCCCATT
1 TGGGCCCATATAGCCCA-T
*
29694140 TCGGCCCATAT
1 TGGGCCCATAT
29694151 GGCCAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (18 bp):
TGGGCCCATATAGCCCAT
Found at i:29694136 original size:18 final size:17
Alignment explanation
Indices: 29694104--29694139 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
29694094 TTGCCTATTA
29694104 TGGGCCCAATAGCCCAT
1 TGGGCCCAATAGCCCAT
*
29694121 TGGGCCCATTTAGCCCAT
1 TGGGCCCA-ATAGCCCAT
29694139 T
1 T
29694140 TCGGCCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.25
Consensus pattern (17 bp):
TGGGCCCAATAGCCCAT
Found at i:29696039 original size:93 final size:93
Alignment explanation
Indices: 29695880--29696050 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
29695870 GCCCTTAAGT
* * * *
29695880 GAACTCGGACTCAACTCAATGAGCTCGGGCATTTGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
29695945 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* **
29695973 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
29696038 CGAGTTCGGATGC
66 CGAGTTCAGATGC
29696051 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:29696040 original size:46 final size:44
Alignment explanation
Indices: 29695877--29696044 Score: 162
Period size: 46 Copynumber: 3.7 Consensus size: 44
29695867 CCCGCCCTTA
* * * *
29695877 AGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGACA-TTGCATCCAT
* *
29695922 AAATGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCAGA---C-A-TTGCATCCAT
*
29695970 CA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCAGACATT-GCATCCAT
29696015 AGGTGAACTCGGACTCAACTCAACGAGTTC
1 A-GTGAACTCGGACTCAACTCAACGAGTTC
29696045 GGATGCTCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 53 0.52
47 29 0.28
48 2 0.02
49 2 0.02
50 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGACATTGCATCCAT
Found at i:29696501 original size:30 final size:30
Alignment explanation
Indices: 29696467--29696526 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
29696457 ATTTAATACG
*
29696467 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTACCCCTA
*** *
29696497 AACTTTTGCATAATTACACTTTTACCCCTA
1 AACTTTAAAAAAATTACACTTTTACCCCTA
29696527 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTACCCCTA
Found at i:29699516 original size:40 final size:39
Alignment explanation
Indices: 29699348--29699518 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
29699338 AGAAATTGAA
* *
29699348 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
29699388 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
29699428 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
29699468 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
29699508 TGATATCCGGG
1 TGATATCCGGG
29699519 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:29707609 original size:40 final size:39
Alignment explanation
Indices: 29707441--29707625 Score: 162
Period size: 40 Copynumber: 4.7 Consensus size: 39
29707431 AGAAATTGAA
* *
29707441 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
29707481 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
29707521 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
29707561 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
29707601 TGATATCCGGG-TAAGTCCCGTAGGC
1 TGATATCCGGGCTAAGACCCGAAGGC
29707626 CTTGGTGCGG
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.03
39 16 0.13
40 95 0.80
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:29714883 original size:46 final size:46
Alignment explanation
Indices: 29714816--29714981 Score: 216
Period size: 46 Copynumber: 3.6 Consensus size: 46
29714806 CCGCCCCTAA
29714816 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
*
29714862 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-
1 GTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT-AG
* *
29714910 -CGAACTCGGACTCAACTCAACGGGTTCGGACATTCGCATCCATAG
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
29714955 GTGAACTCGGACTCAACTCAACGAGTT
1 GTGAACTCGGACTCAACTCAACGAGTT
29714982 TGGAATGCTC
Statistics
Matches: 103, Mismatches: 6, Indels: 22
0.79 0.05 0.17
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 55 0.53
47 28 0.27
48 1 0.01
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAG
Found at i:29715439 original size:30 final size:30
Alignment explanation
Indices: 29715405--29715464 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29715395 ATTTAATACG
29715405 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
29715435 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
29715465 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:29717551 original size:16 final size:17
Alignment explanation
Indices: 29717518--29717556 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
29717508 ACAAAGAAAG
29717518 TTTGGGATTTCAAAATT
1 TTTGGGATTTCAAAATT
* *
29717535 TTTGGG-TTTCGAGATT
1 TTTGGGATTTCAAAATT
29717551 TTTGGG
1 TTTGGG
29717557 GCGTTTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (17 bp):
TTTGGGATTTCAAAATT
Found at i:29720554 original size:29 final size:29
Alignment explanation
Indices: 29720451--29720559 Score: 107
Period size: 29 Copynumber: 3.9 Consensus size: 29
29720441 AATTTCACAT
* * *
29720451 ACATGTATCTGGCCCATTAAGCCC-AATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
* * * * *
29720479 ATATTCATATGACCTATTAGTCCCAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
*
29720508 AC--CTATATGGCCCATTAGGCCCAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
*
29720535 ACATTTATATGGCCCGTTAGGCCCA
1 ACATTTATATGGCCCATTAGGCCCA
29720560 GTCGCATCCA
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
27 22 0.35
28 16 0.26
29 24 0.39
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (29 bp):
ACATTTATATGGCCCATTAGGCCCAAATC
Found at i:29722469 original size:29 final size:29
Alignment explanation
Indices: 29722437--29722571 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
29722427 ATACCCTTCG
** * *
29722437 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
29722466 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
29722495 AGCAT-GCACACTTAGTGCC-TATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
29722523 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
29722552 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
29722572 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
28 25 0.27
29 68 0.72
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:29722532 original size:57 final size:58
Alignment explanation
Indices: 29722441--29722570 Score: 172
Period size: 57 Copynumber: 2.3 Consensus size: 58
29722431 CCTTCGAGCT
** * ** * *
29722441 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* *
29722499 TGCACACTTAGTGCC-TATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
29722556 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
29722571 AATCTCGTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 50 0.81
58 12 0.19
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:29735411 original size:86 final size:86
Alignment explanation
Indices: 29735266--29735440 Score: 314
Period size: 86 Copynumber: 2.0 Consensus size: 86
29735256 CAAATGATTG
*
29735266 TGGAATTCATGAATGGTGAGTTCATGACCATTGTGATAATGTTATTGTGTTAACCTTATGAATAA
1 TGGAATTCATGAATGGTGAGTTCATGACCATTGTGACAATGTTATTGTGTTAACCTTATGAATAA
*
29735331 TGGTATACGTGTATATATGTA
66 TGGTATACGTGTAAATATGTA
*
29735352 TGGAATTCATGAATGGTGAGTTCATGAGCATTGTGACAATGTTATTGTGTTAACCTTATGAATAA
1 TGGAATTCATGAATGGTGAGTTCATGACCATTGTGACAATGTTATTGTGTTAACCTTATGAATAA
*
29735417 TGGTATATGTGTAAATATGTA
66 TGGTATACGTGTAAATATGTA
29735438 TGG
1 TGG
29735441 TAAGAATTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.39
Consensus pattern (86 bp):
TGGAATTCATGAATGGTGAGTTCATGACCATTGTGACAATGTTATTGTGTTAACCTTATGAATAA
TGGTATACGTGTAAATATGTA
Found at i:29737204 original size:42 final size:42
Alignment explanation
Indices: 29737092--29737205 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 42
29737082 TACCATACCA
* **
29737092 ATGCCATATCCCAAATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAAATATGGTCTTACACGAAATCTCATATCG
* * **
29737134 ATGCAAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGC-CATATCCCAAATATGGTCTTACACGAAATCTCATATCG
* *
29737177 ATTCCATATCCCATATATGGTCTTACACG
1 ATGCCATATCCCAAATATGGTCTTACACG
29737206 TACTCTCAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 25 0.42
43 34 0.58
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAAATATGGTCTTACACGAAATCTCATATCG
Found at i:29739127 original size:14 final size:14
Alignment explanation
Indices: 29739108--29739137 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29739098 GTCGATTTAC
29739108 AAAGAATTTCTTAA
1 AAAGAATTTCTTAA
29739122 AAAGAATTTCTTAA
1 AAAGAATTTCTTAA
29739136 AA
1 AA
29739138 TTTAGCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAGAATTTCTTAA
Found at i:29752175 original size:14 final size:14
Alignment explanation
Indices: 29752156--29752192 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29752146 CATACTAAAA
29752156 CTAAGCTTCAATCC
1 CTAAGCTTCAATCC
*
29752170 CTAAGCTTCAATCT
1 CTAAGCTTCAATCC
*
29752184 CAAAGCTTC
1 CTAAGCTTC
29752193 TTGTAAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30
Consensus pattern (14 bp):
CTAAGCTTCAATCC
Found at i:29757767 original size:28 final size:27
Alignment explanation
Indices: 29757681--29757768 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
29757671 AGCATGACTG
* **
29757681 CCAG-AACAGATATTGTGACAGAGTTA
1 CCAGAAACAGATATTGTGGCAGAGCCA
* *
29757707 CCAGATACAGATAATTGTGGTAG-GTCCA
1 CCAGAAACAGAT-ATTGTGGCAGAG-CCA
* *
29757735 TCAGAAATAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATA-TTGTGGCAGAGCCA
29757763 CCAGAA
1 CCAGAA
29757769 CGCTTCCTCC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
26 4 0.09
27 8 0.17
28 34 0.72
29 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (27 bp):
CCAGAAACAGATATTGTGGCAGAGCCA
Found at i:29758870 original size:17 final size:17
Alignment explanation
Indices: 29758848--29758880 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29758838 TCGGTTATGG
29758848 AGAAAAGAAAAGATGAA
1 AGAAAAGAAAAGATGAA
29758865 AGAAAAGAAAAGATGA
1 AGAAAAGAAAAGATGA
29758881 GAAGGGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (17 bp):
AGAAAAGAAAAGATGAA
Found at i:29765605 original size:28 final size:28
Alignment explanation
Indices: 29765542--29765629 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
29765532 AGCATGGCTG
* *
29765542 CCAG-AACAGAT-ATTGTGACAGAGTCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
* * *
29765568 CTAGATACAGATAATTGTGGCAGGGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
*
29765596 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATAATTGTGGCAGAGCCA
29765624 CCAGAA
1 CCAGAA
29765630 CGCTTCCTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.06
27 6 0.12
28 42 0.82
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (28 bp):
CCAGAAACAGATAATTGTGGCAGAGCCA
Found at i:29766731 original size:17 final size:17
Alignment explanation
Indices: 29766709--29766741 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29766699 TCAGCTATAG
29766709 AGAAAAGAAAAGATGAA
1 AGAAAAGAAAAGATGAA
29766726 AGAAAAGAAAAGATGA
1 AGAAAAGAAAAGATGA
29766742 GAAAGGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (17 bp):
AGAAAAGAAAAGATGAA
Found at i:29772627 original size:20 final size:20
Alignment explanation
Indices: 29772602--29772639 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29772592 GTTTATTCGC
*
29772602 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
29772622 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
29772640 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:29774303 original size:28 final size:28
Alignment explanation
Indices: 29774270--29774338 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
29774260 GCGTAGATCA
29774270 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29774298 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29774326 CGATA-TACCCCTA
1 CGAAATTACCCCTA
29774339 GGGTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:29777673 original size:24 final size:24
Alignment explanation
Indices: 29777643--29777909 Score: 435
Period size: 24 Copynumber: 11.1 Consensus size: 24
29777633 GAATGTGACT
* *
29777643 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
29777667 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777691 ATAGTAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
29777715 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777739 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
29777763 ATAGTGAATCGCACACCTAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
29777787 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777811 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777835 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777859 ATAGTAAACCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
29777883 ATAGTAAACCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
29777907 ATA
1 ATA
29777910 TGGTCCTTGC
Statistics
Matches: 232, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 232 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:29783864 original size:20 final size:20
Alignment explanation
Indices: 29783839--29783876 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29783829 GTTTATTCGC
*
29783839 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
29783859 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
29783877 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:29785539 original size:28 final size:28
Alignment explanation
Indices: 29785507--29785561 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
29785497 GTAGATCACG
29785507 AAATTACCCCTAAAGAGCAAAATTACCA
1 AAATTACCCCTAAAGAGCAAAATTACCA
29785535 AAATTACCCCTAAAGAGCAAAATTACC
1 AAATTACCCCTAAAGAGCAAAATTACC
29785562 GATATACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.25, G:0.07, T:0.18
Consensus pattern (28 bp):
AAATTACCCCTAAAGAGCAAAATTACCA
Found at i:29802611 original size:45 final size:45
Alignment explanation
Indices: 29802502--29802676 Score: 234
Period size: 45 Copynumber: 4.0 Consensus size: 45
29802492 CCGAATTCAT
* * *
29802502 TCACCGACATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCA-A
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATA
* *
29802543 TTCACTGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
* *
29802589 TCACCAGCATTATAGCCTGCTAGGCTCAAAGACCCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
29802634 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
29802677 CTGTACGATA
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
42 9 0.08
43 17 0.14
44 5 0.04
45 86 0.72
46 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
Found at i:29803509 original size:75 final size:74
Alignment explanation
Indices: 29803430--29803586 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 74
29803420 AATAAGGGAA
* * *
29803430 AATTTAACCGGAAA-TATTAAGAGCAAATTTAACTGGAATTATTAAGAACAAATTTAA-CTGGAA
1 AATTTAACC-AAAATTATTAAGAGAAAATTTAACCGGAATTATTAAGAACAAATTTAATC-GGAA
29803493 TTATTAAGAAC
64 TTATTAAGAAC
*
29803504 GAATTTAACCAAAATTATTAAGGGAAAATTTAACCGGAATTATTAAGAACAAATTTAATCGGAAT
1 -AATTTAACCAAAATTATTAAGAGAAAATTTAACCGGAATTATTAAGAACAAATTTAATCGGAAT
29803569 TATTAAGAAC
65 TATTAAGAAC
29803579 AATTTAAC
1 AATTTAAC
29803587 AAGCTTAACT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
74 11 0.14
75 64 0.84
76 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.30
Consensus pattern (74 bp):
AATTTAACCAAAATTATTAAGAGAAAATTTAACCGGAATTATTAAGAACAAATTTAATCGGAATT
ATTAAGAAC
Found at i:29803576 original size:25 final size:25
Alignment explanation
Indices: 29803429--29803586 Score: 212
Period size: 25 Copynumber: 6.4 Consensus size: 25
29803419 TAATAAGGGA
* *
29803429 AAATTTAACCGGAAATATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAAC
*
29803454 AAATTTAACTGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
*
29803479 AAATTTAACTGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
* ** *
29803504 GAATTTAACCAAAATTATTAAGGGA-
1 AAATTTAACCGGAATTATTAA-GAAC
29803529 AAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
*
29803554 AAATTTAATCGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
29803579 -AATTTAAC
1 AAATTTAAC
29803587 AAGCTTAACT
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
24 9 0.08
25 106 0.91
26 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (25 bp):
AAATTTAACCGGAATTATTAAGAAC
Found at i:29810236 original size:45 final size:44
Alignment explanation
Indices: 29810113--29810238 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 44
29810103 CAATTCACTA
* *
29810113 GCATTATAGCCTGCTAGGTCGAAGGCCCGAATAGTATATCATCG
1 GCATTATAGCCTGCTAGGTCAAAGGCCCGAATAGTATATCACCG
*
29810157 GCATTATAGCCTGCTAGGGTCAAAGGCCCAAATAGTATATCACCG
1 GCATTATAGCCTGCTA-GGTCAAAGGCCCGAATAGTATATCACCG
**
29810202 GCATTATAGCCTGCTAGGCTCAAAGGCTTGAATAGTA
1 GCATTATAGCCTGCTAGG-TCAAAGGCCCGAATAGTA
29810239 CTGTACGATA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 18 0.24
45 56 0.76
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (44 bp):
GCATTATAGCCTGCTAGGTCAAAGGCCCGAATAGTATATCACCG
Found at i:29811099 original size:25 final size:25
Alignment explanation
Indices: 29811071--29811168 Score: 126
Period size: 25 Copynumber: 4.0 Consensus size: 25
29811061 TAACTTATTT
* *
29811071 GGAAATAATAAGGGCAAATTTAACC
1 GGAAATATTAAGAGCAAATTTAACC
29811096 GGAAATATTAAGAGCAAATTTAACC
1 GGAAATATTAAGAGCAAATTTAACC
* * *
29811121 AGAATTATTAAGAACAAATTTAACC
1 GGAAATATTAAGAGCAAATTTAACC
* *
29811146 GGAATTATTAAGAAC-AATTTAAC
1 GGAAATATTAAGAGCAAATTTAAC
29811169 AAGCTTAACT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
24 8 0.12
25 59 0.88
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (25 bp):
GGAAATATTAAGAGCAAATTTAACC
Found at i:29814257 original size:101 final size:101
Alignment explanation
Indices: 29814093--29814281 Score: 297
Period size: 101 Copynumber: 1.9 Consensus size: 101
29814083 AAGCTCTCTG
* * * *
29814093 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTAACAGTCTGGTACATGTAGTAGCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTAACAATCTAGTACACGTAGTAGCC
* *
29814158 TGCAGTTAGTAATACACACGTGATTGAAGCTATCGA
66 TGAACTTAGTAATACACACGTGATTGAAGCTATCGA
**
29814194 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTAGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTAACAATCTAGTACACGTAGTAGCC
*
29814259 TGAACTTAGTACTACACACGTGA
66 TGAACTTAGTAATACACACGTGA
29814282 CCTACAACCA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (101 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTAACAATCTAGTACACGTAGTAGCC
TGAACTTAGTAATACACACGTGATTGAAGCTATCGA
Found at i:29814258 original size:50 final size:50
Alignment explanation
Indices: 29814100--29814285 Score: 203
Period size: 50 Copynumber: 3.7 Consensus size: 50
29814090 CTGGTACGCA
* ** * * *
29814100 TAGTAGCCTGCACTTAGTACTACACATGCAACCTAACAGTCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTAGTACACG
* * * * * * * *
29814150 TAGTAGCTTGCAGTTAGTAATACACACGTGA-TTGAAGCTATCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CAATCTAGTACACG
*
29814201 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTAGTACACG
*
29814251 TAGTAGCCTGAACTTAGTACTACACACGTGACCTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTA
29814286 CAACCATTTT
Statistics
Matches: 108, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 1 0.01
50 70 0.65
51 36 0.33
52 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTAGTACACG
Found at i:29816333 original size:50 final size:51
Alignment explanation
Indices: 29816269--29816384 Score: 207
Period size: 50 Copynumber: 2.3 Consensus size: 51
29816259 GCAAGGGGTC
29816269 TAATAGATATGGAAATTTAAAGTGGATGTCCTTAAATGGTAACTAGCCCAT
1 TAATAGATATGGAAATTTAAAGTGGATGTCCTTAAATGGTAACTAGCCCAT
29816320 TAAT-GATATGGAAATTTAAAGTGGATGTCCTTAAATGGTAACTAGCCCAT
1 TAATAGATATGGAAATTTAAAGTGGATGTCCTTAAATGGTAACTAGCCCAT
29816370 TAATTAGATAGTGGA
1 TAA-TAGATA-TGGA
29816385 TGATATTGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
50 49 0.79
51 5 0.08
52 4 0.06
53 4 0.06
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (51 bp):
TAATAGATATGGAAATTTAAAGTGGATGTCCTTAAATGGTAACTAGCCCAT
Found at i:29818483 original size:205 final size:205
Alignment explanation
Indices: 29818131--29818542 Score: 806
Period size: 205 Copynumber: 2.0 Consensus size: 205
29818121 CTTTAGCTAC
*
29818131 ATTTGAGGCACTTATGTGCAAAGGTTTTTCTGAGTATCCAATTAGTATTTCAAGTGTTCAACGGG
1 ATTTGAGGCACTTATGTGCAAAGGTTTTTCTGAGTATCCAATTAGTATTCCAAGTGTTCAACGGG
29818196 TAATCCAAGGAAAGAGTTGATGATGGTCCCAATGAGGTAAGGCATTGGTGAGTATGCACTTGAGT
66 TAATCCAAGGAAAGAGTTGATGATGGTCCCAATGAGGTAAGGCATTGGTGAGTATGCACTTGAGT
*
29818261 TATGTTACGAGTTGTGTAGGTATGTACACTAAGCCTATGAGAATTCCTTGGCATGTGATGATCTA
131 TATGTTACGAGTTGTGTAGGTATGTACACTAAGCCCATGAGAATTCCTTGGCATGTGATGATCTA
29818326 TGATGCATAA
196 TGATGCATAA
29818336 ATTTGAGGCACTTATGTGCAAAGGTTTTTCTGAGTATCCAATTAGTATTCCAAGTGTTCAACGGG
1 ATTTGAGGCACTTATGTGCAAAGGTTTTTCTGAGTATCCAATTAGTATTCCAAGTGTTCAACGGG
29818401 TAATCCAAGGAAAGAGTTGATGATGGTCCCAATGAGGTAAGGCATTGGTGAGTATGCACTTGAGT
66 TAATCCAAGGAAAGAGTTGATGATGGTCCCAATGAGGTAAGGCATTGGTGAGTATGCACTTGAGT
29818466 TATGTTACGAGTTGTGTAGGTATGTACACTAAGCCCATGAGAATTCCTTGGCATGTGATGATCTA
131 TATGTTACGAGTTGTGTAGGTATGTACACTAAGCCCATGAGAATTCCTTGGCATGTGATGATCTA
29818531 TGATGCATAA
196 TGATGCATAA
29818541 AT
1 AT
29818543 ATGTGTTCTT
Statistics
Matches: 205, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (205 bp):
ATTTGAGGCACTTATGTGCAAAGGTTTTTCTGAGTATCCAATTAGTATTCCAAGTGTTCAACGGG
TAATCCAAGGAAAGAGTTGATGATGGTCCCAATGAGGTAAGGCATTGGTGAGTATGCACTTGAGT
TATGTTACGAGTTGTGTAGGTATGTACACTAAGCCCATGAGAATTCCTTGGCATGTGATGATCTA
TGATGCATAA
Found at i:29820414 original size:14 final size:14
Alignment explanation
Indices: 29820395--29820425 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29820385 ATAAGATGTT
29820395 AAACTATTAGGGGC
1 AAACTATTAGGGGC
29820409 AAACTATTAGGGGC
1 AAACTATTAGGGGC
29820423 AAA
1 AAA
29820426 TGTGTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (14 bp):
AAACTATTAGGGGC
Found at i:29821489 original size:25 final size:25
Alignment explanation
Indices: 29821461--29821542 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
29821451 ATGATGAATG
29821461 TTTGGTTATGTGTATAGCCATGTGA
1 TTTGGTTATGTGTATAGCCATGTGA
* **
29821486 TTTGGCT-TGTAAAT-G--ATGAATG-
1 TTTGGTTATGTGTATAGCCATG--TGA
29821508 TTTGGTTATGTGTATAGCCATGTGA
1 TTTGGTTATGTGTATAGCCATGTGA
29821533 TTTGGCTTAT
1 TTTGG-TTAT
29821543 TTTGGTATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
21 3 0.07
22 6 0.14
23 8 0.19
24 8 0.19
25 11 0.26
26 7 0.16
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.45
Consensus pattern (25 bp):
TTTGGTTATGTGTATAGCCATGTGA
Found at i:29821497 original size:47 final size:47
Alignment explanation
Indices: 29821428--29821540 Score: 210
Period size: 47 Copynumber: 2.4 Consensus size: 47
29821418 GTAATGGATT
29821428 TAGCCAAT-TGATTTGGCTTGTAAATGATGAATGTTTGGTTATGTGTA
1 TAGCC-ATGTGATTTGGCTTGTAAATGATGAATGTTTGGTTATGTGTA
29821475 TAGCCATGTGATTTGGCTTGTAAATGATGAATGTTTGGTTATGTGTA
1 TAGCCATGTGATTTGGCTTGTAAATGATGAATGTTTGGTTATGTGTA
29821522 TAGCCATGTGATTTGGCTT
1 TAGCCATGTGATTTGGCTT
29821541 ATTTTGGTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
46 2 0.03
47 63 0.97
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (47 bp):
TAGCCATGTGATTTGGCTTGTAAATGATGAATGTTTGGTTATGTGTA
Found at i:29821511 original size:22 final size:22
Alignment explanation
Indices: 29821439--29821512 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
29821429 AGCCAATTGA
29821439 TTTGGCTTGTAAATGATGAATG
1 TTTGGCTTGTAAATGATGAATG
* **
29821461 TTTGGTTATGTGTATAGCCATG--TG
1 TTTGGCT-TGTAAAT-G--ATGAATG
29821485 ATTTGGCTTGTAAATGATGAATG
1 -TTTGGCTTGTAAATGATGAATG
29821508 TTTGG
1 TTTGG
29821513 TTATGTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
21 3 0.08
22 11 0.28
23 8 0.21
24 8 0.21
25 6 0.15
26 3 0.08
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.43
Consensus pattern (22 bp):
TTTGGCTTGTAAATGATGAATG
Found at i:29828288 original size:40 final size:40
Alignment explanation
Indices: 29828244--29828351 Score: 198
Period size: 40 Copynumber: 2.7 Consensus size: 40
29828234 GTGGCTACAT
29828244 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATTCTAC
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATTCTAC
*
29828284 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATTCTAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATTCTAC
*
29828324 CCGGGCTAAGACCCGAAGGCATTTGTGC
1 CCGGGCTAAGACCCGAAGGCATTCGTGC
29828352 ACGTGATTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGATATTCTAC
Found at i:29828365 original size:40 final size:40
Alignment explanation
Indices: 29828197--29828367 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
29828187 TATGCTGGAA
* *
29828197 ATTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAG-T
1 ATTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGAT
** *
29828236 GGCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT
1 -ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT
* *
29828277 ATTCTACCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT
1 ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT
* *
29828317 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACG-T
1 ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GAT
29828356 GATTATATCCGG
1 -ATTATATCCGG
29828368 TTATATTCCG
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.04
40 108 0.95
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAT
Found at i:29831002 original size:22 final size:22
Alignment explanation
Indices: 29830977--29831021 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29830967 CTCTTAGTTC
*
29830977 TTTAAG-TATTATCTTTATGGGT
1 TTTAAGCTATT-TCTTAATGGGT
*
29830999 TTTAGGCTATTTCTTAATGGGT
1 TTTAAGCTATTTCTTAATGGGT
29831021 T
1 T
29831022 CTATCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (22 bp):
TTTAAGCTATTTCTTAATGGGT
Found at i:29832174 original size:27 final size:27
Alignment explanation
Indices: 29832070--29832197 Score: 125
Period size: 27 Copynumber: 4.7 Consensus size: 27
29832060 CCGATTTTTA
* * ** *
29832070 AAATTATTGAAATACCCCCAGGTTGTA
1 AAATTATCGAAATACCCCTAATTTGTG
* *
29832097 AAATTATTGAAATATCCCTAATTTGTG
1 AAATTATCGAAATACCCCTAATTTGTG
* *
29832124 AAATTACCGAAATA-CCCTCGATTTGTG
1 AAATTATCGAAATACCCCT-AATTTGTG
*
29832151 AAATTATCGAAATACCCCTTATTTGTG
1 AAATTATCGAAATACCCCTAATTTGTG
*
29832178 AAATTA-CTGAAATACACCTA
1 AAATTATC-GAAATACCCCTA
29832198 TGGGGTAGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
26 5 0.06
27 77 0.90
28 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (27 bp):
AAATTATCGAAATACCCCTAATTTGTG
Found at i:29832227 original size:26 final size:27
Alignment explanation
Indices: 29832187--29832284 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 27
29832177 GAAATTACTG
* *
29832187 AAATACACCTATGGGGTA-GATTACCT
1 AAATACCCCTGTGGGGTAGGATTACCT
* *
29832213 AAAAACCCCTGTGGGGCAGGATTA-CT
1 AAATACCCCTGTGGGGTAGGATTACCT
* * *
29832239 GAAATACCCCTATGGAGTAGGATTACCG
1 -AAATACCCCTGTGGGGTAGGATTACCT
* *
29832267 AAATACCCTTGTAGGGTA
1 AAATACCCCTGTGGGGTA
29832285 AAATGACCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
26 16 0.29
27 39 0.70
28 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
AAATACCCCTGTGGGGTAGGATTACCT
Found at i:29832337 original size:26 final size:26
Alignment explanation
Indices: 29832279--29832343 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
29832269 ATACCCTTGT
*
29832279 AGGGTAAAATGACCATTTTGCCCTAA
1 AGGGTAAAATGACTATTTTGCCCTAA
** *
29832305 AAAGTAAAATGACTATTTTGCCCTTA
1 AGGGTAAAATGACTATTTTGCCCTAA
*
29832331 TGGGT-AAATGACT
1 AGGGTAAAATGACT
29832344 GACTTGGGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (26 bp):
AGGGTAAAATGACTATTTTGCCCTAA
Found at i:29834503 original size:61 final size:61
Alignment explanation
Indices: 29834430--29834552 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
29834420 TTTGGGTGTT
29834430 TGCAAAATTTTAATTTTTGGGCTCTTAAGTGAACTTGGATGTTAGCTTATAGGACTTATAA
1 TGCAAAATTTTAATTTTTGGGCTCTTAAGTGAACTTGGATGTTAGCTTATAGGACTTATAA
*
29834491 TGCAAAATTTTAATTTTTGGGTTCTTAAGTGAACTTGGATGTTAGCTTATAGGACTTATAA
1 TGCAAAATTTTAATTTTTGGGCTCTTAAGTGAACTTGGATGTTAGCTTATAGGACTTATAA
29834552 T
1 T
29834553 AATTAGTGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (61 bp):
TGCAAAATTTTAATTTTTGGGCTCTTAAGTGAACTTGGATGTTAGCTTATAGGACTTATAA
Found at i:29835136 original size:22 final size:22
Alignment explanation
Indices: 29835111--29835155 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29835101 CTCTTAGTTC
*
29835111 TTTAAG-TATTATCTTTATGGGT
1 TTTAAGCTATT-TCTTAATGGGT
*
29835133 TTTAGGCTATTTCTTAATGGGT
1 TTTAAGCTATTTCTTAATGGGT
29835155 T
1 T
29835156 CTATCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (22 bp):
TTTAAGCTATTTCTTAATGGGT
Found at i:29836252 original size:27 final size:27
Alignment explanation
Indices: 29836235--29836326 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
29836225 TAAAATTATT
29836235 GAAATACCCTTGATTTGTGAAATTACC
1 GAAATACCCTTGATTTGTGAAATTACC
* * *
29836262 AAAATACCCTCGATTTGTGAAATTACT
1 GAAATACCCTTGATTTGTGAAATTACC
* *
29836289 GAAATACCCTCT-ATTTGTGAAACTATC
1 GAAATACCCT-TGATTTGTGAAATTACC
29836316 GAAATACCCTT
1 GAAATACCCTT
29836327 ATGGGGTAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 55 0.98
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (27 bp):
GAAATACCCTTGATTTGTGAAATTACC
Done.